[gmx-users] Parametrisation of the heteroatomic pdb

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 10 10:01:12 CET 2011


On 10/11/2011 7:36 PM, James Starlight wrote:
> Thanks Mark,
>
> 1) By the way do you know any database where I could obtain 
> information about function of the specific CAP groups ?
> E.g as I know the most spread CAP on N is ACE group but in my case 
> there is For ( simple COH group) instead of ACE.
>
> I think that parametrisation of such simple groups should not be very 
> complicate but it's strange that I've not found already built topology 
> for them.

People use acetyl rather than formyl cap either because that's what was 
used in the experimental system, or because they are simulating a 
fragment from a larger peptide and acetyl makes for a better model of a 
peptide bond than formyl for only a small extra cost. I don't even know 
that any force fields have parameters for H-C(O)-N(H)-R. I suggest you 
use acetyl.

>
>
> 2) Also I've tried to made topology for D amoniacids. I've started 
> with the topology of L analogs e.g for D-val I've created enty based 
> on the Val in .rtp and .hdb files. Not I think I should to invert 
> impropers for the Calpha atoms that new topology represent to true 
> D-isomer :) But I'm not sure about how to make it correctly :)
>
> In .itp I've found for new DVA residue
>
>  [ impropers ]
> ;  ai    aj    ak    al   gromos type
>     N    -C    CA     H     gi_1
>    CA     N     C    CB     gi_2
>    CA   CG1   CG2    CB     gi_2
>     C    CA    +N     O     gi_1
>
> here there are 2 enties for the Ca atoms. What should I do with it for 
> invertion?

First, identify that there's anything to invert. Look at the #define 
lines for gi_1 and gi_2 and the manual sections for impropers. There's 
nothing associated with any handedness. The impropers for chirality 
prevent inversion, rather than enforcing a particular chirality. You can 
test this yourself. Make a .tpr of an L-amino acid and .gro files of 
each chirality, and then use mdrun -rerun Lconfiguration.gro -s 
Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s 
Lconfiguration.

Mark

>
> James
>
>
> 2011/11/10 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     On 10/11/2011 7:05 PM, James Starlight wrote:
>>     Justin,
>>
>>
>>     I've also look for the cap editing in the pymol but it seems that
>>     that function lacks in that program
>>
>>     By the way, what are specificity of such Cap groups ? Do they are
>>     only sheld charges on the termi or have something addition function?
>
>     They can. The purpose of a simulation is to provide a model of
>     reality. How one would wish to cap a peptide depends what is being
>     modelled under what conditions with what objectives in mind.
>
>
>>
>>     What difference beetwen different caps I cant understand why in
>>     my structure there are so non-standart groups.
>
>     Shrug. We don't even know what they are... Wherever you sourced
>     your starting structure should discuss how and why the termini
>     have such caps.
>
>     Mark
>
>
>>
>>
>>     James
>>
>>     2011/11/9 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>>         James Starlight wrote:
>>
>>             Justin,
>>
>>             Could you tell me another alternative ways to replace
>>             existing cap groups in my pdb besides xleap ? ( I've had
>>              many problems with the pdb's processed by this soft).
>>             Also I've tried to make topology for the non-standart
>>             caps by PRODRG but I also have some problems with such
>>             parametrisation.
>>
>>
>>         Unless you describe your problems, there's very little anyone
>>         can or will try to do to help you.  I've never had a problem
>>         with an xleap coordinate file, so I can't offer you any
>>         additional guidance with that.  Otherwise, there are dozens
>>         of programs that are capable of drawing molecules or editing
>>         files.  See, for instance:
>>
>>         http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
>>
>>         -Justin
>>
>>
>>             Also I've not found suitable topology for some D-isomers
>>             ( it's strange that parametriation for such typical
>>             non-standart residues is absent in all force fields ). As
>>             I understood I cant use topology of L-analogs for the
>>             parametrisation of such D-forms because I dont know
>>             suitable parameters for dihedrals for instance.
>>             Have someone pre-built parameters for the D-aa for Gromos
>>             or Charmm force field?
>>
>>
>>             Thanks,
>>
>>             James
>>
>>             2011/10/29 Justin A. Lemkul <jalemkul at vt.edu
>>             <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>>             <mailto:jalemkul at vt.edu>>>
>>
>>
>>
>>
>>                James Starlight wrote:
>>
>>                    Justin, hello!
>>
>>                    Could you tell me what exactly program from the
>>             Amber tools
>>                    package you've used for the KALP peptide
>>             preparation e.g for
>>                    capping ?
>>
>>
>>                xleap
>>
>>                At this point, please start a new thread for your
>>             questions, as
>>                these topics are completely unrelated to where you
>>             started.
>>
>>                -Justin
>>
>>
>>                --     ==============================__==========
>>
>>
>>                Justin A. Lemkul
>>                Ph.D. Candidate
>>                ICTAS Doctoral Scholar
>>                MILES-IGERT Trainee
>>                Department of Biochemistry
>>                Virginia Tech
>>                Blacksburg, VA
>>                jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
>>             (540) 231-9080
>>             http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin <http://vt.edu/Pages/Personal/justin>
>>             <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>>                ==============================__==========
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>>         -- 
>>         ========================================
>>
>>         Justin A. Lemkul
>>         Ph.D. Candidate
>>         ICTAS Doctoral Scholar
>>         MILES-IGERT Trainee
>>         Department of Biochemistry
>>         Virginia Tech
>>         Blacksburg, VA
>>         jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>         ========================================
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